Rhabdomyosarcoma (RMS) is a family of pediatric soft tissue tumors related to the skeletal muscle lineage. There have been incremental improvements in outcome over the last three decades, such that cure is now possible for ~70% of newly diagnosed RMS patients. A risk-adapted therapy system has been developed for RMS with risk assessment based on pre-surgical stage, post-surgical group, presence of distal metastases, and histologic subtype. Beyond these clinical indicators of cancer status, molecular markers are now being evaluated to provide further improvement in risk prediction. This application focuses on analysis of minimal disseminated disease in which PCR-based assays of tumor-specific molecular markers permit sensitive detection of tumor cell spread to sites such as bone marrow. For RMS, several small studies used RNA-based PCR methods to demonstrate the feasibility of detecting RMS cells in bone marrow in patients without clinical evidence of metastatic disease. Furthermore, there is evidence from these and other studies that detection of occult tumor cells in the bone marrow is predictive of a worse outcome. To fully understand the utility of this approach in RMS management, these minimal disseminated disease assays must be conducted as part of large well-controlled clinical trials. In an effort to pursue this goal, bone marrow and peripheral blood samples were collected in the recently completed Children's Oncology Group D9803 trial of intermediate risk RMS. Due to the time required for the centralized collection protocol, the RNA in these specimens was often partially degraded. However, the DNA in these samples is still intact and this project will develop DNA-based assays applicable to RMS. DNA hypermethylation is a DNA modification that is often tumor-specific at numerous genomic loci. It can be detected by a PCR-based methodology that has been used to screen for occult cancer cells in multiple cancer types. Based on preliminary evidence that DNA hypermethylation occurs at specific loci in both RMS subtypes, a microarray strategy will be used to screen for genomic loci that are frequently hypermethylated in RMS tumors but not in normal blood cells. These findings will be confirmed and refined by PCR-based assays. To extend these findings, a small panel of quantitative methylation-specific PCR assays will be designed that detect at least one methylation change in most RMS tumors. This panel of quantitative PCR assays will be applied to DNA from the D9803 bone marrow samples as well as a panel of paired primary tumors. The results of these assays will be compared with clinical and pathological characteristics as well as patient outcome to explore the significance of minimal disseminated disease in the bone marrow at diagnosis. This application thus creates a valuable opportunity to identify, develop and test new assays, and then apply these assays to perform correlative laboratory studies on an existing set of annotated biospecimens that are part of an important clinical initiative of the Soft Tissue Sarcoma Committee of the Children's Oncology Group. PUBLIC HEALTH RELEVANCE: This research project directly focuses on the pediatric cancer rhabdomyosarcoma, and proposes an approach to identify patients with early spread of this cancer to distal sites. In this approach, DNA will be isolated from a tissue to which cancer cells often spread, such as bone marrow, and will be screened for the presence of cancer cells by assaying for genetic changes that commonly occur in the cancer but not in the normal version of that tissue. The value of this approach will then be investigated by using these assays on a series of bone marrow samples from a clinical trial of the Children's Oncology Group, and then comparing the assay results with the patients'outcome data.